Nativity scenes are plentiful in San Cristóbal de las Casas, a colonial city in the highlands of Chiapas, Mexico. But the one that greets visitors at the entrance to the TierrAdentro cultural centre has a local twist: figurines on donkeys wear miniature ski masks and carry wooden guns.

It is high season for "Zapatourism", the industry of international travellers that has sprung up around the indigenous uprising here, and TierrAdentro is ground zero. Zapatista-made weavings, posters and jewellery are selling briskly. In the courtyard restaurant, where the mood at 10pm is festive, verging on fuzzy, college students drink Sol beer. A young man holds up a photograph of the rebel leader, Subcomandante Marcos, as always in a mask with a pipe, and kisses it. As he does so, his friends snap yet another picture of this most documented of movements.

I am taken through the revellers to a room at the back of the cultural centre, closed to the public. The sombre mood here seems a world away. Ernesto Ledesma Arronte, a 40-year-old ponytailed researcher, is hunched over military maps and human rights incident reports. "Did you understand what Marcos said?" he asks me. "It was very strong. He hasn't said anything like that in many years."

Ledesma Arronte is referring to a speech that Marcos made the night before, at a conference outside San Cristóbal. The speech was titled Feeling Red: the Calendar and the Geography of War. Because it was Marcos, it was poetic and slightly elliptical. But to Ledesma Arronte's ears, it was a code-red alert. "Those of us who have made war know how to recognise the paths by which it is prepared and brought near," Marcos said. "The signs of war on the horizon are clear. War, like fear, also has a smell. And now we are starting to breathe its foetid odour in our lands."

Marcos's assessment supports what Ledesma Arronte and his fellow researchers at the Centre of Political Analysis and Social and Economic Investigations have been tracking with their maps and charts. On the 56 permanent military bases that the Mexican state runs on indigenous land in Chiapas, there has been a marked increase in activity. Weapons and equipment are being dramatically upgraded and new battalions are moving in, including special forces - all signs of escalation.

As the Zapatistas became a global symbol for a new model of resistance, it was possible to forget that the war in Chiapas never actually ended. For his part, Marcos - despite his clandestine identity - has been playing a defiantly open role in Mexican politics, most notably during the fiercely contested 2006 presidential elections. Rather than endorsing the centre-left candidate, Andrés Manuel López Obrador, he spearheaded a parallel "Other Campaign", holding rallies that called attention to issues ignored by the major candidates.

In this period, Marcos's role as military leader of the Zapatista Army of National Liberation (EZLN) seemed to fade into the background. He was Delegate Zero - the anti-candidate. The previous evening, Marcos had announced that the conference would be his last such appearance for some time. "Look, the EZLN is an army," he reminded his audience, and he is its "military chief".

That army faces a grave new threat - one that cuts to the heart of the Zapatistas' struggle. During the 1994 uprising, the EZLN claimed large stretches of land and collectivised them, its most tangible victory.

In the San Andrés accords of 1996, the right to territory was recognised, but the Mexican government has refused to fully ratify the accords. After failing to enshrine these rights, the Zapatistas decided to turn them into facts on the ground. They formed their own government structures - good government councils - and stepped up the building of autonomous schools and clinics. As the Zapatistas expand their role as the de facto government in large areas of Chiapas, the federal and state government's determination to undermine them is intensifying.

"Now," says Ledesma Arronte, "they have their method." The method is to use the deep desire for land among all peasants in Chiapas against the Zapatistas. Ledesma Arronte's organisation has documented the ways in which, in just one region, the government has spent approximately $16m expropriating land, before passing it on - to members of the many families linked to the notoriously corrupt Institutional Revolutionary party (PRI). Often, the land is already occupied by Zapatista families. Most ominously, many of the new "owners" are linked to thuggish paramilitary groups, which are trying to force the Zapatistas from the newly titled land.

Since September there has been a marked escalation in violence, including shots fired into the air, brutal beatings, and Zapatista families reporting being threatened with death, rape and dismemberment. Soon the soldiers in their barracks may well have the excuse they need to descend: restoring "peace" among feuding indigenous groups. For months, the Zapatistas have been resisting violence and trying to expose these provocations. But by choosing not to line up behind López Obrador in the 2006 election, the movement made powerful enemies. And now, says Marcos, their calls for help are being met with a deafening silence.

Exactly 10 years ago, on December 22 1997, as part of the anti-Zapatista campaign, a paramilitary gang opened fire in a small church in the village of Acteal, killing 45 indigenous people, 16 of them children and adolescents. Some of the bodies were hacked with machetes. The state police heard the gunfire and did nothing. For weeks now, Mexico's newspapers have been filled with articles marking the anniversary of the massacre.

In Chiapas, however, many people point out that conditions today feel eerily familiar: the paramilitaries, the rising tension, the mysterious activities of soldiers, the renewed isolation from the rest of the country. And they have a plea to those who supported them in the past: don't just look back. Look forward, and prevent another Acteal massacre before it happens.